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M2M Final Exam > Unit I - Cell Biology > Flashcards

Unit I - Cell Biology Flashcards

1
Q

Intron splice site consensus sequences

A

GU marks the 5’ end of an intron

AG marks the 3’ end of an intron

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2
Q

Spliceosome

A

Made of small nuclear ribonuclear proteins (snRPS) and snRNAs

U1 snRNA contains a sequence complementary to the mRNA sequence near the 5’ splice site of introns

U2 snRNA base pairs with the intron at a point corresponding to the branch point A residue, activating it for nucleophilic attack

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3
Q

Purine accumulation disorders

A

Defect in hypoxanthine-guanine phosphoribosyl transferase (HGPT); leads to accumulation of purines (uric acid) in tissues

Gout
Lesch-Nyhan Syndrome

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4
Q

Deamination of 5mC and C

A

Deamination of 5-methyl cytosine converts 5mC to thymine

Deamination of C yields U

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5
Q

Puromycin

A

Antibiotic; inhibits bacterial translation by mimicking the 3; tRNA acceptor region and interacting with the ribosome to cause premature peptide release

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6
Q

Functions of RNA Poly I, II, III

A

RNA Polymerase I - synthesizes pre-ribosomal RNA

RNA Polymerase II - synthesizes mRNA

RNA Polymerase III - synthesizes tRNA

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7
Q

TATA Box / Initiator sequence

A

DNA control element located 25-30bp upstream from the transcription start site; bound by TATa-binding protein (TBP); this is the site at which general TFs bind

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8
Q

TFIID

A

Contains TATA-binding protein (TBP) as well as TBP-associated factors (TAFs)

Part of RNA Polymerase II pre-initiation complex

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9
Q

Rifampicin

A

Antibiotic; binds to RNA polymerase at the exit channel and sterically occludes the formation of mRNA chains > 2-3 nucleotides long

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10
Q

TFIIF

A

Phosphorylates RNA Polymerase II, which activates it

Part of RNA Polymerase II pre-initiation complex

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11
Q

TFIIH

A

CDK7 subunit phosphorylates Pol II CTD; has some helicase activity and functions in nucleotide excision repair (NER)

Part of RNA Polymerase II pre-initiation complex

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12
Q

Nucleotide Excision Repair (NER)

A

Removes DNA lesions that distort the DNA structure (i.e. dimers) and therefore block RNA or DNA polymerase from binding

Cockayne Syndrome & Xeroderma Pigmentosum are caused by defects in NER, often TFIIH

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13
Q

PolyA tail cleavage site consensus sequence

A

AAUAAA 10 to 30 nucleotides upstream from the cleavage site

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14
Q

DNA Polymerase III

A

The main polymerase involved in DNA replication; Pol III “holds on” to the DNA via a sliding clamp protein and has 3-5’ exonuclease activity that enables proofreading

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15
Q

DNA Polymerase I

A

Mostly involved in replacing RNA primer with DNA; has exonuclease activity in the 5-3; direction

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16
Q

DNA Mismatch repair

A

MutS/MutL (in prokaryotes) or MSH/LH (in eukaryotes) recognize mismatched DNA nucleotides on the newly synthesized strand, which is unmethylated

Defects in this pathway cause hereditary non-polyposis colorectal cancer (HNPCC)/Lynch Syndrome

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17
Q

Base Excision Repair (BER)

A

Removes DNA lesions that do not cause distortions in the backbone and therefore may be missed by NER; glycosylase enzymes hydrolyze the N-glycosidic bond to remove the damaged base, producing an AP site which is removed by AP-specific endonuclease

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18
Q

Homologous Recombination & Non-homologous end joining (NHEJ)

A

Both repair double-stranded DNA breaks; HR repairs breaks between homologous ends; it requires the presence of a homologous chromosome (S & G2 phase)

NHEJ repairs breaks between non-homologous ends, which may lead to insertion/deletion of nucleotides at the break point

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19
Q

4 categories of DNA binding domains

A

Helix-Turn-Helix (Homeodomain)
Zinc Finger
Basic Leucine Zipper Proteins (bZLP)
Basic Helix-Loop-Helix motif (bHLH)

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20
Q

Histone structure

A

Histones are octameric proteins consisting of dimers of subunits H2A, H2B, H3, and H4

Histone H1 is bound to linker DNA between histones and functions to “slide” histones along DNA during modification

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21
Q

Histone De/Acetylation

A

Histone Acetyltransferases (HATs) and Histone De-acetyltransferases (HDATs) are classes of reversible chromatin modifiers; acetylation of histone N-termini Lysine residues neutralizes the positive charge and “frees” the histone tails from electrostatic reactions with the DNA phosphate backbone

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22
Q

Stop Codons

A

UAA
UAG
UGA

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23
Q

Shine-Delgarno Sequence

A

Prokaryotic ribosomal binding site; essentially corresponds with initiator AUG codon

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24
Q

Initiation Factor 4E (IF4E)

A

Binds the 7-methyl guanosine cap on the 5’ end of the mRNA, facilitating scanning of the ribosome down the primary transcript to the start AUG codon

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25
Q

Elongation Factors (Prok and Euk)

A

Ef-Tu (in bacteria) & Ef1A (in eukaryotes); deliver charged aa-tRNA complexes to the A site of the ribosome, burning GTP when it dissociates

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26
Q

Initiation of Translation - Bacteria

A

IF1 and IF3 bind the small subunit, which binds the mRNA at the AUG start codon via base pairing with the Shine Delgarno sequence

IF2 (bound to GTP) delivers initiation Met-tRNA to the P site to pair with the AUG codon

GTP hydrolysis on IF2 releases all IFs and signals binding of the large subunit

27
Q

DNA Polymerase delta

A

Performs DNA synthesis on the lagging strand in eukaryotes; contains 3-5’ exonuclease activity

28
Q

DNA Polymerase alpha

A

Functions in the synthesis of the first ~20 DNA nucleotides immediately following the RNA primers; also synthesizes the first basepairs of each Okazaki fragment

DNA polymerase alpha has primase activity

29
Q

DNA Polymerase epsilon

A

Performs DNA synthesis on the leading strand in eukaryotes; contains 3-5’ exonuclease activity

30
Q

Release Factor (RF)

A

Enters the A site (bound to GTP) in conjunction with a stop codon; hydrolysis of GTP induces release of the ribosomal subunits

31
Q

Sources & Types of High Energy Bonds

A 
Thioester bonds (i.e. Acetyl coA)
Phosphoanydride bonds (i.e. ATP) 
Phosphoenolpyruvate (PEP)
32
Q

Relationship between free energy, enthalpy, and entropy of a system

A

dG = dH - TdS

33
Q

Reduction Potential (E)

A

A measure of the willingness of a molecule to become reduced; the more positive the value of E, the more likely a molecule is to accept electrons (become reduced); the more negative the value of E, the more likely a molecule is to donate electrons (become oxidized)

Energy is released as electrons pass from compounds with low E to high E values

34
Q

Relationship between free energy and redox potential

A

dG = -nFdE

35
Q

Enzyme cofactor vs. coenzyme

A

Cofactors are small molecules (often metal ions) that function with an enzyme to catalyze a reaction; cofactors are not used up in the reaction

Coenzymes provide chemical groups for a catalyzed reaction; they are used up by the reaction

Prosthetic groups are cofactors/coenzymes that are tightly bound to the enzyme

36
Q

Km

A

Km is the substrate concentration at which Vo = 1/2(Vmax)

Km typically approximates intracellular concentrations of [S]

37
Q

Kcat

A

Kcat describes the number of substrate molecules turned into product per enzyme molecule, per second, at saturating substrate concentrations

The larger the Kcat value, the faster the enzyme works to turnover

38
Q

Kcat/Km

A

A measure comparing enzyme efficiency; the larger the value of Kcat/Km, the more efficient the enzyme

Enzymes that are “catalytically perfect” have a Kcat value approaching 10^8; the enzyme is so efficient that rate of diffusion is the only limiting factor

39
Q

Inhibitors - 3 classifications

A

Competitive - Bind to the enzyme active site, blocking binding of the natural substrate

Uncompetitive - Bind to the ES complex at a site other than the active site

Mixed - May bind to either E or ES at a site other than the active site

40
Q

Alpha Helix

A

H-bonds form between the carbonyl oxygen of the nth AA and the amide nitrogen of the n + 4th AA within the same polypeptide chain, forming a right-handed screw

Ala and Leu are commonly found; Pro and Gly do not occur

41
Q

Beta Sheets

A

Secondary structure motif formed by hydrogen bonds between two polypeptide chains running parallel or anti-parallel to each other

Ex: Immunoglobulin, antibodies

42
Q

Kd

A

Dissociation constant; Kd is the ligand concentration at which 50% of the protein is ligand-bound

Smaller Kd value implies a stronger binding interaction

43
Q

Myoglobin

A

Stores oxygen; oxygen binds Fe2+ in the heme group, which is buried within the myoglobin protein; Kd is very low, so myoglobin stores oxygen but does not transport

44
Q

Hemoglobin

A

Hb has 4 O2 binding sites that interact with allostery; O2 binding triggers a T to R conformational state change in which Hb has higher affinity for O2

Hb binds O2 better under local conditions of higher pH (i.e. in the lungs) and releases O2 under conditions of lower pH (i.e. in metabolically active tissues)

45
Q

2 Classes of Chaperone Proteins

A
  1. HSP70 - binds to the hydrophobic regions of unfolded proteins, preventing aggregation and facilitating re-folding
  2. GroEl/GroES (prok) / HSP60 (euks) - forms a capped, barrel-like structure that isolates mis-folded proteins and hydrolyzes ATP to aid in re-folding
46
Q

Alzheimers - 3 primary genetic pathways

A
  1. Missense mutation in APP gene causes increased production of all B-amyloid proteins, including B-42 via cleavage by B-secretase and y-secretase
  2. ApoE4 genetic variant leads to decreased AB 42 clearance
  3. Mutation in presenelin genes, leading to increased production of AB42 (more common in familial cases of Alzheimers)
47
Q

Stages of the Cell Cycle

A

G1 - Cell growth; building and loading of Pre-RC onto origin
S - Activation of Pre-Rc, DNA Synthesis
G2 - Protein synthesis and cell growth
M - Chromosome Segregation

48
Q

Rad 17, ATM/ATR, p53, p21, Rb cycle

A

Rad17 senses & binds to damaged DNA, recruiting ATM/ATR

ATM/ATR proteins kinases phosphorylate p53

Phosphorylated p53 is a TF that promotes synthesis of p21, a CDK inhibitor

p21 inhibits CDK, which fails to phosphorylate Rb

Unphosphorylated Rb binds to and inhibits transcription factor E2F, which is necessary for transcription of a group of genes involved in DNA synthesis

In response to DNA damage the cell is held in G1 phase and cannot progress to S phase

49
Q

Pre-RC Cycle

A

Pre-RC is built and loaded onto replication origins in G1; Pre-RC are activated during S phase

This ensures that cells may not replicate and divide during the same phase of the cell cycle

50
Q

VDJ Recombination

A

An endogenous source of double stranded DNA breaks responsible for generation of diversity in immunoglobulin DNA via non-homologous end joining; mutations in NHEJ genes lead to severe combined immunodeficiency (SCID) because functional B-cells and T-cells are not produced

51
Q

Crohn’s Disease

A

Most often affects the Ileum & Colon, although may affect the entire GI tract

Characterized by: discontinuous lesions, transmural inflammation, perianal disease, strictures & fistulas

52
Q

Ulcerative Colitis

A

Most often affects the colon & rectum

Characterized by: continuous lesions, mucosal inflammation, hematochezia

53
Q

Extra-GI manifestations of Crohn’s / Ulcerative Colitis

A

Infections of the eyes - Iritis, episcleritis
Infections of the lungs & heart - pleuritis, myocarditis
Pancreatitis
Ankylosing Spondylitis (chronic inflammatory arthritis)
Sacroileitis
Erythema Nodosum - inflammation of subcutaneous fat (usually on shins)
Pyoderma gangrenosum (chronic ulcers on the legs)

54
Q

Swi/Snf

A

Chromatin remodeling complex that uses DNA to break histone/DNA contacts and slide the histones down the DNA, “loosening” the chromatin structure

55
Q

Tetracycline, Streptomycin, Erythromycin

A

Antibiotic drugs that bind to the small subunit of the prokaryotic ribosome, preventing entry of aa-tRNAs into the A site and thus inhibiting bacterial protein synthesis

56
Q

Interferon

A

Interferon is released by cells in response to viral infection; in neighboring cells, it stimulates the activity of kinases which phosphosrylates eIF2; when phosphorylated, eIF2 is bound by eIF2-BP and initiation of translation is stalled

57
Q

eIF2

A

A eukaryotic initiation factor required for translation; eIF2 mediates the binding of the initiator t-Met complex to the ribosomal P site; after formation of the proper codon-anticodon pairing, eIF2 hydrolyzes GTP and releases from the ribosome

58
Q

Ciclosporin

A

An immunosuppressant drug; ciclosporin binds to cyclophilin, inhibiting activation of calcineurin; normally, calcineurin functions to dephosphorylate the transcription factor NFAT, allowing it to move to the nucleus and activate transcription of genes coding for immune cell proliferation; ciclosporin therefore prevents translocation of the TF NFAT

59
Q

Rubenstein-Taybi Syndrome

A

Results from mutations in one copy of the CREB-BP gene; CREB-BP is a transcriptional co-activator for many TFs and is a HAT; presents as cognitive disability & craniofacial dysmorphism

60
Q

a-aminitin toxin

A

Death cap mushroom toxin; blocks the translocation of RNA polymerase II by interacting with its bridge helix

61
Q

Tamoxifen

A

Tamoxifen antagonizes estrogen by binding to the estrogen receptor (ER) and preventing recruitment of HAT co-factors (activators)

62
Q

NFKB Pathway

A

NFKB protein is usually held in the cytoplasm by binding to its inhibitor (IKB); phosphorylation of IKB targets it for degradation, releasing NFKB to move into the nucleus where it turns on its target genes, including genes involved in inflammation

Aspirin inhibits the phosphorylation of IKB

63
Q

Rapamycin

A

An immunosuppressant drug; Inhibits mTOR (mammalian target of Rapamycin), which is a kinase that phosphorylates 4E-BP; inhibition of mTOR leads to dephosphorylation of 4E-BP, which is the state in which it binds eIF4E, silencing translation

M2M Final Exam (9 decks)

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